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Python 0.5.7

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@github-actions github-actions released this 17 Jun 17:26
· 143 commits to main since this release

Breaking Changes

  • The VCF writing methods (ts.write_vcf, ts.as_vcf) now error if a site with
    position zero is encountered. The VCF spec does not allow zero position sites.
    Suppress this error with the allow_position_zero argument.
    (@benjeffery, #2901, #2838)

Bugfixes

  • Fix to the folded, expected allele frequency spectrum (i.e.,
    TreeSequence.allele_frequency_spectrum(mode="branch", polarised=False),
    which was half as big as it should have been. (@petrelharp,
    @nspope, #2933)